Another noteable, not only is it the only place I buy my books, it is also independantly owned. :)
Powells refuses to sell out to the man! wooo. They also have a smaller and less known outlet on Hawthorn St. as well I believe.

In addition to its location on W Burnside at 10th, Powell's Books does indeed have a smaller store on SE Hawthorne Blvd (with an E... I live one block from it), as well as locations at PDX (The Portland Airport), Washington Square mall in Beaverton, a travel bookstore in Pioneer Courthouse Square (downtown at SW 6th and Yamhill), and a technical bookstore on the North Park Blocks at NW Park and Couch.

Another interesting note about Powells is that, while it has a reputation as being counter-culture and anti-corporate, they have been acting very poorly towards their employees. Recently they were on strike. Their main complaint was that the average wage at Powells, including the high payed computer geeks at Powells.com was on the order of $8 an hour. They voted to unionize and Powell (the man behind the store), for a long time, refused to recognize the union.
It was a very odd thing to cross a picket line to go to a book store. I promised the striking workers who accosted me in the street that I would browse a lot, and leave books in the wrong place, but not buy anthing. That seemed to make them smile.
They now have a contract so we can all shop at Powells again without feeling guilty.

A side note about powells.com:

If you've spent much time on the web site, you'll notice that someone at Powell's Books has an inordinate fondness for Pokey the Penguin. At the end of each URL, you'll see the following:

...&pokey=skeptopotamus

I emailed the webmaster about this as soon as I discovered Pokey the Penguin. Was this really a reference to the comic strip, and why on earth was it being appended to the URL anyhow?

The answer: Yes, a former web programmer was a big fan of Pokey. Setting pokey to "skeptopotamus" allows a cookie to record where you've been so that you can resume searching from where you left off.

Now you know... and knowing is half the battle!

(qousqous has another take on this at Powell's and Pokey.)